Constructing carbon nanotubes (CNTs) manually can be time-consuming and error-prone, especially when trying to align repeating molecular building blocks with sub-angstrom precision. For researchers and students working in nanotechnology, computational chemistry, or molecular modeling, producing realistic nanoscale architectures often involves a lot of manual tweaking—unless the right tools are used.
The Pattern Editors in SAMSON can significantly simplify this process. With intuitive visual widgets and replication tools, you can build intricate structures such as nanotubes in just a few steps. Here, we walk through a concrete example of manually constructing a carbon nanotube using SAMSON’s built-in editors.
Why do this manually?
While SAMSON also includes a dedicated Carbon Nanotube Editor, understanding how to manually build a nanotube helps you learn how to customize patterns, replicate units with control over geometry, and construct other architectures beyond preset tools. It’s flexible and educational.
Step-by-Step: Building a Carbon Nanotube
- Create a base ring: Use SAMSON’s tools to build a carbon ring (e.g. a benzene-like ring). Remove hydrogen atoms and rotate the ring so its edges align cleanly in the XY plane.
- Use the Circular Pattern Editor: Activate the editor (W) and set the number of instances—typically 12 or more—to form a closed ring. Adjust the radius until bonding atoms are nearly touching. Once you’re satisfied, click Accept to merge overlapping atoms and close the loop.
- Align the ring: Using the
Edit > Alignfeature, ensure the entire ring lies flat in the XY plane. This alignment is helpful for creating a stable and symmetric tube when stacking layers. - Stack the rings linearly: Activate the Linear Pattern Editor (L). Translate along the Z-axis (2 Å is a common spacing) to position the next ring. If needed, apply a small rotational offset to match bond angles across layers. Use the mouse wheel or keystrokes to adjust the number of copies. Accept to finalize.
- Optimize geometry: Open the minimization tool to relax the structure and eliminate small overlaps or strain. You can also automatically add hydrogen atoms back if needed.
Using these editors, you can manually build a clean, realistic nanotube in minutes. Even better, the visual widgets provide subtle visual feedback, allowing you to fine-tune transformations interactively.
What else can this approach be used for?
This isn’t just for CNTs. The same method applies to other repetitive or cyclic nanoscale architectures. Whether you’re arranging DNA origami paths, tiling nanostructures, or modeling polymeric spirals, pattern editors give you precise control over positioning and orientation.
To learn more about these editors and other use cases—like curved pattern creation or advanced distribution tools—visit the full documentation:
https://documentation.samson-connect.net/users/latest/creating-patterns/
SAMSON and all SAMSON Extensions are free for non-commercial use. You can get SAMSON at https://www.samson-connect.net.